In Covid19R/coronavirus: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

knitr::opts_chunk$set(
  collapse = TRUE, 
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  fig.path = "man/figures/README-",
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coronavirus

The coronavirus package provides a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic. The raw data pulled from the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus repository.

More details available here, and a csv format of the package dataset available here

A summary dashboard is available here

Source: Centers for Disease Control and Prevention's Public Health Image Library

Important Note

As this an ongoing situation, frequent changes in the data format may occur, please visit the package news to get updates about those changes

Installation

Install the CRAN version:

install.packages("coronavirus")

Install the Github version (refreshed on a daily bases):

# install.packages("devtools")
devtools::install_github("RamiKrispin/coronavirus")

Data refresh

While the coronavirus CRAN version is updated every month or two, the Github (Dev) version is updated on a daily bases. The update_dataset function enables to overcome this gap and keep the installed version with the most recent data available on the Github version:

library(coronavirus)
update_dataset()

Note: must restart the R session to have the updates available

Usage

data("coronavirus")

This coronavirus dataset has the following fields:

head(coronavirus) 
tail(coronavirus)

Here is an example of a summary total cases by region and type (top 20):

library(dplyr)

summary_df <- coronavirus %>% group_by(Country.Region, type) %>%
  summarise(total_cases = sum(cases)) %>%
  arrange(-total_cases)

summary_df %>% head(20)

Summary of new cases during the past 24 hours by country and type (as of r max(coronavirus$date)):

library(tidyr)

coronavirus %>% 
  filter(date == max(date)) %>%
  select(country = Country.Region, type, cases) %>%
  group_by(country, type) %>%
  summarise(total_cases = sum(cases)) %>%
  pivot_wider(names_from = type,
              values_from = total_cases) %>%
  arrange(-confirmed)

Data Sources

The raw data pulled and arranged by the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) from the following resources:

World Health Organization (WHO): https://www.who.int/
DXY.cn. Pneumonia. 2020. http://3g.dxy.cn/newh5/view/pneumonia.
BNO News: https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/
National Health Commission of the People’s Republic of China (NHC): http:://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml
China CDC (CCDC): http:://weekly.chinacdc.cn/news/TrackingtheEpidemic.htm
Hong Kong Department of Health: https://www.chp.gov.hk/en/features/102465.html
Macau Government: https://www.ssm.gov.mo/portal/
Taiwan CDC: https://sites.google.com/cdc.gov.tw/2019ncov/taiwan?authuser=0
US CDC: https://www.cdc.gov/coronavirus/2019-ncov/index.html
Government of Canada: https://www.canada.ca/en/public-health/services/diseases/coronavirus.html
Australia Government Department of Health: https://www.health.gov.au/news/coronavirus-update-at-a-glance
European Centre for Disease Prevention and Control (ECDC): https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases